IGFL3

IGF like family member 3, the group of IGF like family

Basic information

Region (hg38): 19:46120067-46124688

Links

ENSG00000188624 ∙ NCBI:388555 ∙ OMIM:610546 ∙ HGNC:32930 ∙ Uniprot:Q6UXB1 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the IGFL3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the IGFL3 gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous						0
missense			17	1		18
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	17	1	0

Variants in IGFL3

This is a list of pathogenic ClinVar variants found in the IGFL3 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
19-46123892-C-T		not specified	Uncertain significance (Jan 08, 2024)
19-46123915-G-C		not specified	Uncertain significance (Sep 04, 2024)
19-46123920-A-C		not specified	Uncertain significance (Sep 28, 2022)
19-46123920-A-G		not specified	Uncertain significance (Oct 29, 2021)
19-46123968-G-T		not specified	Uncertain significance (Dec 19, 2023)
19-46123973-C-T		not specified	Uncertain significance (Dec 28, 2024)
19-46123979-G-A		not specified	Uncertain significance (Jun 27, 2022)
19-46124019-A-C		not specified	Uncertain significance (Mar 29, 2022)
19-46124021-G-T		not specified	Likely benign (Feb 27, 2024)
19-46124024-G-C		not specified	Uncertain significance (Mar 25, 2024)
19-46124033-C-T		not specified	Uncertain significance (Aug 07, 2024)
19-46124034-G-A		not specified	Uncertain significance (Aug 27, 2024)
19-46124051-G-T		not specified	Uncertain significance (Mar 31, 2024)
19-46124108-C-T		not specified	Uncertain significance (Apr 19, 2023)
19-46124120-G-A		not specified	Uncertain significance (Feb 14, 2023)
19-46124154-C-T		not specified	Uncertain significance (Dec 09, 2023)
19-46124315-A-G		not specified	Uncertain significance (Mar 31, 2023)
19-46124637-A-G		not specified	Uncertain significance (Aug 26, 2024)
19-46124639-C-T		not specified	Uncertain significance (Jun 02, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
IGFL3	protein_coding	protein_coding	ENST00000341415	4	4604

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0120	0.861	125492	0	17	125509	0.0000677

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.147	67	70.5	0.951	0.00000384	796
Missense in Polyphen		31	30.692	1.01		362
Synonymous	-0.567	31	27.2	1.14	0.00000143	240
Loss of Function	1.25	4	7.77	0.515	4.28e-7	85

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000325	0.000324
Ashkenazi Jewish	0.0000994	0.0000992
East Asian	0.0000547	0.0000546
Finnish	0.00	0.00
European (Non-Finnish)	0.0000265	0.0000264
Middle Eastern	0.0000547	0.0000546
South Asian	0.00	0.00
Other	0.000331	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Potential ligand of the IGFLR1 cell membrane receptor. {ECO:0000269|PubMed:21454693}.

Intolerance Scores

• loftool: 0.689
• rvis_EVS: 0.37
• rvis_percentile_EVS: 74.95

Haploinsufficiency Scores

• pHI: 0.0810
• hipred: N
• hipred_score: 0.139
• ghis: 0.397

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.144

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Igfl3

Gene ontology

• Biological process: biological_process
• Cellular component: extracellular space
• Molecular function: signaling receptor binding